OpenRaiser/Intern-Atlas huggingface dataset:
Evolution of Hierarchical Structure & Reuse in iGEM Synthetic DNA Sequences
Venue: arXiv cs.NE 2019
Year: 2019

Many complex systems, both in technology and nature, exhibit hierarchical modularity: smaller modules, each of them providing a certain function, are used within larger modules that perform more complex functions. Previously, we have proposed a modeling framework, referred to as Evo-Lexis, that provides insight to some fundamental questions about evolving hierarchical systems. The predictions of the Evo-Lexis model should be tested using real data from evolving systems in which the outputs can be well represented by sequences. In this paper, we investigate the time series of iGEM synthetic DNA dataset sequences, and whether the resulting iGEM hierarchies exhibit the qualitative properties predicted by the Evo-Lexis framework. Contrary to Evo-Lexis, in iGEM the amount of reuse decreases during the timeline of the dataset. Although this results in development of less cost-efficient and less deep Lexis-DAGs, the dataset exhibits a bias in reusing specific nodes more often than others. This results in the Lexis-DAGs to take the shape of an hourglass with relatively high H-score values and stable set of core nodes. Despite the reuse bias and stability of the core set, the dataset presents a high amount of diversity among the targets which is in line with modeling of Evo-Lexis.
Kinematic & Dynamic Analysis of the Human Upper Limb Using the Theory of Screws
Venue: arXiv cs.RO 2019
Year: 2019

Screw theory provides geometrical insight into the mechanics of rigid bodies. Screw axis is defined as the line coinciding with the joint axis. Line transformations in the form of a screw operator are used to determine the joint axes of a seven degree of freedom manipulator, representing the human upper limb. Multiplication of a unit screw axis with the joint angular velocity provides the joint twist. Instantaneous motion of a joint is the summation of the twists of the preceding joints and the joint twist itself. Inverse kinematics, velocities and accelerations are calculated using the screw Jacobian for a non-redundant six degree of freedom manipulator. Netwon and Euler dynamic equations are then utilized to solve for the forward and inverse dynamic problems. Dynamics of the upper limb and the upper limb combined with an exoskeleton are only different due to the additional mass and inertia of the exoskeleton. Dynamic equations are crucial for controlling the exoskeleton in position and force.
Second-order Co-occurrence Sensitivity of Skip-Gram with Negative Sampling
Venue: arXiv cs.CL 2019
Year: 2019

We simulate first- and second-order context overlap and show that Skip-Gram with Negative Sampling is similar to Singular Value Decomposition in capturing second-order co-occurrence information, while Pointwise Mutual Information is agnostic to it. We support the results with an empirical study finding that the models react differently when provided with additional second-order information. Our findings reveal a basic property of Skip-Gram with Negative Sampling and point towards an explanation of its success on a variety of tasks.
Covariance in Physics and Convolutional Neural Networks
Venue: arXiv cs.LG 2019
Year: 2019

In this proceeding we give an overview of the idea of covariance (or equivariance) featured in the recent development of convolutional neural networks (CNNs). We study the similarities and differences between the use of covariance in theoretical physics and in the CNN context. Additionally, we demonstrate that the simple assumption of covariance, together with the required properties of locality, linearity and weight sharing, is sufficient to uniquely determine the form of the convolution.
Fine-Grained Entity Typing in Hyperbolic Space
Venue: arXiv cs.CL 2019
Year: 2019

How can we represent hierarchical information present in large type inventories for entity typing? We study the ability of hyperbolic embeddings to capture hierarchical relations between mentions in context and their target types in a shared vector space. We evaluate on two datasets and investigate two different techniques for creating a large hierarchical entity type inventory: from an expert-generated ontology and by automatically mining type co-occurrences. We find that the hyperbolic model yields improvements over its Euclidean counterpart in some, but not all cases. Our analysis suggests that the adequacy of this geometry depends on the granularity of the type inventory and the way hierarchical relations are inferred.
Contextual Relabelling of Detected Objects
Venue: arXiv cs.CV 2019
Year: 2019

Contextual information, such as the co-occurrence of objects and the spatial and relative size among objects provides deep and complex information about scenes. It also can play an important role in improving object detection. In this work, we present two contextual models (rescoring and re-labeling models) that leverage contextual information (16 contextual relationships are applied in this paper) to enhance the state-of-the-art RCNN-based object detection (Faster RCNN). We experimentally demonstrate that our models lead to enhancement in detection performance using the most common dataset used in this field (MSCOCO).
Measuring the compositionality of noun-noun compounds over time
Venue: arXiv cs.CL 2019
Year: 2019

We present work in progress on the temporal progression of compositionality in noun-noun compounds. Previous work has proposed computational methods for determining the compositionality of compounds. These methods try to automatically determine how transparent the meaning of the compound as a whole is with respect to the meaning of its parts. We hypothesize that such a property might change over time. We use the time-stamped Google Books corpus for our diachronic investigations, and first examine whether the vector-based semantic spaces extracted from this corpus are able to predict compositionality ratings, despite their inherent limitations. We find that using temporal information helps predicting the ratings, although correlation with the ratings is lower than reported for other corpora. Finally, we show changes in compositionality over time for a selection of compounds.
Localizing Catastrophic Forgetting in Neural Networks
Venue: arXiv cs.LG 2019
Year: 2019

Artificial neural networks (ANNs) suffer from catastrophic forgetting when trained on a sequence of tasks. While this phenomenon was studied in the past, there is only very limited recent research on this phenomenon. We propose a method for determining the contribution of individual parameters in an ANN to catastrophic forgetting. The method is used to analyze an ANNs response to three different continual learning scenarios.
Impact of Prior Knowledge and Data Correlation on Privacy Leakage: A Unified Analysis
Venue: arXiv cs.LG 2019
Year: 2019

It has been widely understood that differential privacy (DP) can guarantee rigorous privacy against adversaries with arbitrary prior knowledge. However, recent studies demonstrate that this may not be true for correlated data, and indicate that three factors could influence privacy leakage: the data correlation pattern, prior knowledge of adversaries, and sensitivity of the query function. This poses a fundamental problem: what is the mathematical relationship between the three factors and privacy leakage? In this paper, we present a unified analysis of this problem. A new privacy definition, named \textit{prior differential privacy (PDP)}, is proposed to evaluate privacy leakage considering the exact prior knowledge possessed by the adversary. We use two models, the weighted hierarchical graph (WHG) and the multivariate Gaussian model to analyze discrete and continuous data, respectively. We demonstrate that positive, negative, and hybrid correlations have distinct impacts on privacy leakage. Considering general correlations, a closed-form expression of privacy leakage is derived for continuous data, and a chain rule is presented for discrete data. Our results are valid for general linear queries, including count, sum, mean, and histogram. Numerical experiments are presented to verify our theoretical analysis.
Energy Predictive Models with Limited Data using Transfer Learning
Venue: arXiv cs.LG 2019
Year: 2019

In this paper, we consider the problem of developing predictive models with limited data for energy assets such as electricity loads, PV power generations, etc. We specifically investigate the cases where the amount of historical data is not sufficient to effectively train the prediction model. We first develop an energy predictive model based on convolutional neural network (CNN) which is well suited to capture the interaday, daily, and weekly cyclostationary patterns, trends and seasonalities in energy assets time series. A transfer learning strategy is then proposed to address the challenge of limited training data. We demonstrate our approach on a usecase of daily electricity demand forecasting. we show practicing the transfer learning strategy on the CNN model results in significant improvement to existing forecasting methods.
Machine Learning and Visualization in Clinical Decision Support: Current State and Future Directions
Venue: arXiv cs.LG 2019
Year: 2019

Deep learning, an area of machine learning, is set to revolutionize patient care. But it is not yet part of standard of care, especially when it comes to individual patient care. In fact, it is unclear to what extent data-driven techniques are being used to support clinical decision making (CDS). Heretofore, there has not been a review of ways in which research in machine learning and other types of data-driven techniques can contribute effectively to clinical care and the types of support they can bring to clinicians. In this paper, we consider ways in which two data driven domains - machine learning and data visualizations - can contribute to the next generation of clinical decision support systems. We review the literature regarding the ways heuristic knowledge, machine learning, and visualization are - and can be - applied to three types of CDS. There has been substantial research into the use of predictive modeling for alerts, however current CDS systems are not utilizing these methods. Approaches that leverage interactive visualizations and machine-learning inferences to organize and review patient data are gaining popularity but are still at the prototype stage and are not yet in use. CDS systems that could benefit from prescriptive machine learning (e.g., treatment recommendations for specific patients) have not yet been developed. We discuss potential reasons for the lack of deployment of data-driven methods in CDS and directions for future research.
Attention is all you need for Videos: Self-attention based Video Summarization using Universal Transformers
Venue: arXiv cs.CV 2019
Year: 2019

Video Captioning and Summarization have become very popular in the recent years due to advancements in Sequence Modelling, with the resurgence of Long-Short Term Memory networks (LSTMs) and introduction of Gated Recurrent Units (GRUs). Existing architectures extract spatio-temporal features using CNNs and utilize either GRUs or LSTMs to model dependencies with soft attention layers. These attention layers do help in attending to the most prominent features and improve upon the recurrent units, however, these models suffer from the inherent drawbacks of the recurrent units themselves. The introduction of the Transformer model has driven the Sequence Modelling field into a new direction. In this project, we implement a Transformer-based model for Video captioning, utilizing 3D CNN architectures like C3D and Two-stream I3D for video extraction. We also apply certain dimensionality reduction techniques so as to keep the overall size of the model within limits. We finally present our results on the MSVD and ActivityNet datasets for Single and Dense video captioning tasks respectively.
From Caesar Cipher to Unsupervised Learning: A New Method for Classifier Parameter Estimation
Venue: arXiv cs.LG 2019
Year: 2019

Many important classification problems, such as object classification, speech recognition, and machine translation, have been tackled by the supervised learning paradigm in the past, where training corpora of parallel input-output pairs are required with high cost. To remove the need for the parallel training corpora has practical significance for real-world applications, and it is one of the main goals of unsupervised learning. Recently, encouraging progress in unsupervised learning for solving such classification problems has been made and the nature of the challenges has been clarified. In this article, we review this progress and disseminate a class of promising new methods to facilitate understanding the methods for machine learning researchers. In particular, we emphasize the key information that enables the success of unsupervised learning - the sequential statistics as the distributional prior in the labels. Exploitation of such sequential statistics makes it possible to estimate parameters of classifiers without the need of paired input-output data. In this paper, we first introduce the concept of Caesar Cipher and its decryption, which motivated the construction of the novel loss function for unsupervised learning we use throughout the paper. Then we use a simple but representative binary classification task as an example to derive and describe the unsupervised learning algorithm in a step-by-step, easy-to-understand fashion. We include two cases, one with Bigram language model as the sequential statistics for use in unsupervised parameter estimation, and another with a simpler Unigram language model. For both cases, detailed derivation steps for the learning algorithm are included. Further, a summary table compares computational steps of the two cases in executing the unsupervised learning algorithm for learning binary classifiers.
Inductive Bias of Gradient Descent based Adversarial Training on Separable Data
Venue: arXiv cs.LG 2019
Year: 2019

Adversarial training is a principled approach for training robust neural networks. Despite of tremendous successes in practice, its theoretical properties still remain largely unexplored. In this paper, we provide new theoretical insights of gradient descent based adversarial training by studying its computational properties, specifically on its inductive bias. We take the binary classification task on linearly separable data as an illustrative example, where the loss asymptotically attains its infimum as the parameter diverges to infinity along certain directions. Specifically, we show that when the adversarial perturbation during training has bounded $\ell_2$-norm, the classifier learned by gradient descent based adversarial training converges in direction to the maximum $\ell_2$-norm margin classifier at the rate of $\tilde{\mathcal{O}}(1/\sqrt{T})$, significantly faster than the rate $\mathcal{O}(1/\log T)$ of training with clean data. In addition, when the adversarial perturbation during training has bounded $\ell_q$-norm for some $q\ge 1$, the resulting classifier converges in direction to a maximum mixed-norm margin classifier, which has a natural interpretation of robustness, as being the maximum $\ell_2$-norm margin classifier under worst-case $\ell_q$-norm perturbation to the data. Our findings provide theoretical backups for adversarial training that it indeed promotes robustness against adversarial perturbation.
Key Ingredients of Self-Driving Cars
Venue: arXiv cs.RO 2019
Year: 2019

Over the past decade, many research articles have been published in the area of autonomous driving. However, most of them focus only on a specific technological area, such as visual environment perception, vehicle control, etc. Furthermore, due to fast advances in the self-driving car technology, such articles become obsolete very fast. In this paper, we give a brief but comprehensive overview on key ingredients of autonomous cars (ACs), including driving automation levels, AC sensors, AC software, open source datasets, industry leaders, AC applications and existing challenges.
Object-Agnostic Suction Grasp Affordance Detection in Dense Cluster Using Self-Supervised Learning.docx
Venue: arXiv cs.RO 2019
Year: 2019

In this paper we study grasp problem in dense cluster, a challenging task in warehouse logistics scenario. By introducing a two-step robust suction affordance detection method, we focus on using vacuum suction pad to clear up a box filled with seen and unseen objects. Two CNN based neural networks are proposed. A Fast Region Estimation Network (FRE-Net) predicts which region contains pickable objects, and a Suction Grasp Point Affordance network (SGPA-Net) determines which point in that region is pickable. So as to enable such two networks, we design a self-supervised learning pipeline to accumulate data, train and test the performance of our method. In both virtual and real environment, within 1500 picks (~5 hours), we reach a picking accuracy of 95% for known objects and 90% for unseen objects with similar geometry features.
Visual Person Understanding through Multi-Task and Multi-Dataset Learning
Venue: arXiv cs.CV 2019
Year: 2019

We address the problem of learning a single model for person re-identification, attribute classification, body part segmentation, and pose estimation. With predictions for these tasks we gain a more holistic understanding of persons, which is valuable for many applications. This is a classical multi-task learning problem. However, no dataset exists that these tasks could be jointly learned from. Hence several datasets need to be combined during training, which in other contexts has often led to reduced performance in the past. We extensively evaluate how the different task and datasets influence each other and how different degrees of parameter sharing between the tasks affect performance. Our final model matches or outperforms its single-task counterparts without creating significant computational overhead, rendering it highly interesting for resource-constrained scenarios such as mobile robotics.
CoAPI: An Efficient Two-Phase Algorithm Using Core-Guided Over-Approximate Cover for Prime Compilation of Non-Clausal Formulae
Venue: arXiv cs.AI 2019
Year: 2019

Prime compilation, i.e., the generation of all prime implicates or implicants (primes for short) of formulae, is a prominent fundamental issue for AI. Recently, the prime compilation for non-clausal formulae has received great attention. The state-of-the-art approaches generate all primes along with a prime cover constructed by prime implicates using dual rail encoding. However, the dual rail encoding potentially expands search space. In addition, constructing a prime cover, which is necessary for their methods, is time-consuming. To address these issues, we propose a novel two-phase method -- CoAPI. The two phases are the key to construct a cover without using dual rail encoding. Specifically, given a non-clausal formula, we first propose a core-guided method to rewrite the non-clausal formula into a cover constructed by over-approximate implicates in the first phase. Then, we generate all the primes based on the cover in the second phase. In order to reduce the size of the cover, we provide a multi-order based shrinking method, with a good tradeoff between the small size and efficiency, to compress the size of cover considerably. The experimental results show that CoAPI outperforms state-of-the-art approaches. Particularly, for generating all prime implicates, CoAPI consumes about one order of magnitude less time.
Reliable Estimation of Individual Treatment Effect with Causal Information Bottleneck
Venue: arXiv cs.LG 2019
Year: 2019

Estimating individual level treatment effects (ITE) from observational data is a challenging and important area in causal machine learning and is commonly considered in diverse mission-critical applications. In this paper, we propose an information theoretic approach in order to find more reliable representations for estimating ITE. We leverage the Information Bottleneck (IB) principle, which addresses the trade-off between conciseness and predictive power of representation. With the introduction of an extended graphical model for causal information bottleneck, we encourage the independence between the learned representation and the treatment type. We also introduce an additional form of a regularizer from the perspective of understanding ITE in the semi-supervised learning framework to ensure more reliable representations. Experimental results show that our model achieves the state-of-the-art results and exhibits more reliable prediction performances with uncertainty information on real-world datasets.
Joint QoS-control and Handover Optimization in Backhaul aware SDN-based LTE Networks
Venue: arXiv cs.NI 2019
Year: 2019

Future cellular networks will be dense and require key traffic management technologies for fine-grained network control. The problem gets more complicated in the presence of different network segments with bottleneck links limiting the desired quality of service (QoS) delivery to the last mile user. In this work, we first design a framework for software-defined cellular networks (SDCN) and then propose new mechanisms for management of QoS and non-QoS users traffic considering both access and backhaul networks, jointly. The overall SDN-LTE system and related approaches are developed and tested using network simulator (ns-3) in different network environments. Especially, when the users are non-uniformly distributed, the results shows that compared to other approaches, the proposed load distribution algorithm enables at least 6\% and 23\% increase in the average QoS user downlink (DL) throughput for all network users and 40\%-ile edge users, respectively. Also, the proposed system efficiently achieves desired QoS and handles the network congestion without incurring significant overhead.
Analyzing Social Media Data to Understand Consumers' Information Needs on Dietary Supplements
Venue: arXiv cs.CY 2019
Year: 2019

Despite the high consumption of dietary supplements (DS), there are not many reliable, relevant, and comprehensive online resources that could satisfy information seekers. The purpose of this research study is to understand consumers' information needs on DS using topic modeling and to evaluate its accuracy in correctly identifying topics from social media. We retrieved 16,095 unique questions posted on Yahoo! Answers relating to 438 unique DS ingredients mentioned in sub-section, "Alternative medicine" under the section, "Health". We implemented an unsupervised topic modeling method, Correlation Explanation (CorEx) to unveil the various topics consumers are most interested in. We manually reviewed the keywords of all the 200 topics generated by CorEx and assigned them to 38 health-related categories, corresponding to 12 higher-level groups. We found high accuracy (90-100%) in identifying questions that correctly align with the selected topics. The results could be used to guide us to generate a more comprehensive and structured DS resource based on consumers' information needs.
Building a Production Model for Retrieval-Based Chatbots
Venue: arXiv cs.CL 2019
Year: 2019

Response suggestion is an important task for building human-computer conversation systems. Recent approaches to conversation modeling have introduced new model architectures with impressive results, but relatively little attention has been paid to whether these models would be practical in a production setting. In this paper, we describe the unique challenges of building a production retrieval-based conversation system, which selects outputs from a whitelist of candidate responses. To address these challenges, we propose a dual encoder architecture which performs rapid inference and scales well with the size of the whitelist. We also introduce and compare two methods for generating whitelists, and we carry out a comprehensive analysis of the model and whitelists. Experimental results on a large, proprietary help desk chat dataset, including both offline metrics and a human evaluation, indicate production-quality performance and illustrate key lessons about conversation modeling in practice.